DESeq Analysis on EGME small RNA data (New)
Overview
Perform DESeq2 and related analysis on 6 different datasets: * miRNA counts generated by sRNAde * miRNA counts parsed from sRNAbench (the same data as above, but with more miRNAs) * ncRNA counts parsed from sRNAbench * tRNA counts parsed from sRNAbench * cDNA counts parsed from sRNAbench * a dataset contains all types of small RNAs using another dataset
For each of the dataset, perform the following preprocessing procedure: 1. remove Library_24 and Library_33, as by QC they have problems like low counts 2. filter out small RNAs with less than 10 counts across all libraries
miRNA from sRNAde
We first analyze the miRNA read counts generated by sRNAde.
sample-wise heatmap
- rows and columns clustered
- label = library+dosages
PCA plots
- From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder.
- The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18) /folder.
- It is interesting that the datapoints labeled with dosage roughly form a spectrum on PC1.
DESeq with Wald test
- dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## Wald test p-value: dosage 50 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-200b-3p 48.78561 1.653585 0.349556 4.73053 2.23931e-06
## rno-miR-221-3p 29.41731 2.122209 0.493184 4.30308 1.68439e-05
## rno-let-7c-5p 163.30752 1.419720 0.409246 3.46911 5.22186e-04
## rno-miR-429 19.94727 1.403375 0.412940 3.39850 6.77570e-04
## rno-miR-365-3p 7.72493 1.821033 0.553912 3.28759 1.01049e-03
## rno-miR-205 31.13048 1.544480 0.491664 3.14133 1.68181e-03
## rno-miR-23a-3p 108.38653 0.975798 0.327285 2.98150 2.86843e-03
## rno-miR-24-3p 58.19679 1.244753 0.422272 2.94775 3.20092e-03
## rno-let-7b-5p 79.33072 1.089664 0.384765 2.83203 4.62538e-03
## rno-miR-871-3p 8.09010 1.445964 0.535561 2.69990 6.93593e-03
## padj
## <numeric>
## rno-miR-200b-3p 0.000179145
## rno-miR-221-3p 0.000673754
## rno-let-7c-5p 0.013551409
## rno-miR-429 0.013551409
## rno-miR-365-3p 0.016167902
## rno-miR-205 0.022424138
## rno-miR-23a-3p 0.032009227
## rno-miR-24-3p 0.032009227
## rno-let-7b-5p 0.041114465
## rno-miR-871-3p 0.055487445- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## Wald test p-value: dosage 60 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-221-3p 29.4173 3.54509 0.500999 7.07605 1.48319e-12
## rno-miR-200b-3p 48.7856 2.20786 0.359500 6.14149 8.17489e-10
## rno-miR-429 19.9473 2.46121 0.419608 5.86550 4.47774e-09
## rno-miR-205 31.1305 2.92857 0.500489 5.85142 4.87391e-09
## rno-miR-10a-5p 114.3573 2.08064 0.357632 5.81783 5.96174e-09
## rno-miR-24-3p 58.1968 2.34332 0.432226 5.42152 5.90941e-08
## rno-miR-145-5p 289.3245 1.90685 0.354328 5.38161 7.38218e-08
## rno-miR-23a-3p 108.3865 1.72876 0.335978 5.14545 2.66874e-07
## rno-miR-22-3p 54.7086 2.40169 0.480464 4.99869 5.77211e-07
## rno-miR-320-3p 14.7781 2.78132 0.574202 4.84380 1.27376e-06
## padj
## <numeric>
## rno-miR-221-3p 1.18655e-10
## rno-miR-200b-3p 3.26996e-08
## rno-miR-429 9.53879e-08
## rno-miR-205 9.53879e-08
## rno-miR-10a-5p 9.53879e-08
## rno-miR-24-3p 7.87921e-07
## rno-miR-145-5p 8.43678e-07
## rno-miR-23a-3p 2.66874e-06
## rno-miR-22-3p 5.13077e-06
## rno-miR-320-3p 1.01901e-05- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## Wald test p-value: dosage 75 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-200b-3p 48.7856 2.88793 0.363240 7.95049 1.85769e-15
## rno-miR-429 19.9473 3.27752 0.425455 7.70356 1.32323e-14
## rno-miR-221-3p 29.4173 3.78480 0.508133 7.44843 9.44541e-14
## rno-miR-10a-5p 114.3573 2.59696 0.359572 7.22237 5.10891e-13
## rno-miR-205 31.1305 3.20308 0.507005 6.31765 2.65576e-10
## rno-miR-23a-3p 108.3865 1.76838 0.340275 5.19692 2.02616e-07
## rno-miR-29a-3p 87.5367 1.79645 0.361240 4.97299 6.59268e-07
## rno-miR-22-3p 54.7086 2.41307 0.485496 4.97031 6.68446e-07
## rno-miR-10b-5p 91.1628 1.44507 0.292337 4.94315 7.68687e-07
## rno-miR-871-3p 8.0901 2.65986 0.565270 4.70546 2.53291e-06
## padj
## <numeric>
## rno-miR-200b-3p 1.48615e-13
## rno-miR-429 5.29293e-13
## rno-miR-221-3p 2.51878e-12
## rno-miR-10a-5p 1.02178e-11
## rno-miR-205 4.24922e-09
## rno-miR-23a-3p 2.70154e-06
## rno-miR-29a-3p 6.68446e-06
## rno-miR-22-3p 6.68446e-06
## rno-miR-10b-5p 6.83278e-06
## rno-miR-871-3p 1.91822e-05Volcano plots for DESeq with Wald test
DESeq with likelihood ratio test
Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.
- dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-429 19.9473 1.403375 0.412940 64.1291 7.70233e-14
## rno-miR-200b-3p 48.7856 1.653585 0.349556 60.4358 4.74383e-13
## rno-miR-10a-5p 114.3573 0.918542 0.349446 59.0682 9.29613e-13
## rno-miR-221-3p 29.4173 2.122209 0.493184 58.1286 1.47558e-12
## rno-miR-205 31.1305 1.544480 0.491664 44.3393 1.27839e-09
## rno-miR-22-3p 54.7086 0.297279 0.473674 42.1150 3.79283e-09
## rno-miR-145-5p 289.3245 0.682316 0.345690 34.6466 1.44673e-07
## rno-miR-23a-3p 108.3865 0.975798 0.327285 32.4929 4.11984e-07
## rno-miR-10b-5p 91.1628 0.301981 0.280696 31.5731 6.43782e-07
## rno-miR-24-3p 58.1968 1.244753 0.422272 30.3081 1.18870e-06
## padj
## <numeric>
## rno-miR-429 6.16186e-12
## rno-miR-200b-3p 1.89753e-11
## rno-miR-10a-5p 2.47897e-11
## rno-miR-221-3p 2.95117e-11
## rno-miR-205 2.04543e-08
## rno-miR-22-3p 5.05711e-08
## rno-miR-145-5p 1.65340e-06
## rno-miR-23a-3p 4.11984e-06
## rno-miR-10b-5p 5.72250e-06
## rno-miR-24-3p 9.50960e-06- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-429 19.9473 2.46121 0.419608 64.1291 7.70233e-14
## rno-miR-200b-3p 48.7856 2.20786 0.359500 60.4358 4.74383e-13
## rno-miR-10a-5p 114.3573 2.08064 0.357632 59.0682 9.29613e-13
## rno-miR-221-3p 29.4173 3.54509 0.500999 58.1286 1.47558e-12
## rno-miR-205 31.1305 2.92857 0.500489 44.3393 1.27839e-09
## rno-miR-22-3p 54.7086 2.40169 0.480464 42.1150 3.79283e-09
## rno-miR-145-5p 289.3245 1.90685 0.354328 34.6466 1.44673e-07
## rno-miR-23a-3p 108.3865 1.72876 0.335978 32.4929 4.11984e-07
## rno-miR-10b-5p 91.1628 1.05431 0.288295 31.5731 6.43782e-07
## rno-miR-24-3p 58.1968 2.34332 0.432226 30.3081 1.18870e-06
## padj
## <numeric>
## rno-miR-429 6.16186e-12
## rno-miR-200b-3p 1.89753e-11
## rno-miR-10a-5p 2.47897e-11
## rno-miR-221-3p 2.95117e-11
## rno-miR-205 2.04543e-08
## rno-miR-22-3p 5.05711e-08
## rno-miR-145-5p 1.65340e-06
## rno-miR-23a-3p 4.11984e-06
## rno-miR-10b-5p 5.72250e-06
## rno-miR-24-3p 9.50960e-06- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-429 19.9473 3.27752 0.425455 64.1291 7.70233e-14
## rno-miR-200b-3p 48.7856 2.88793 0.363240 60.4358 4.74383e-13
## rno-miR-10a-5p 114.3573 2.59696 0.359572 59.0682 9.29613e-13
## rno-miR-221-3p 29.4173 3.78480 0.508133 58.1286 1.47558e-12
## rno-miR-205 31.1305 3.20308 0.507005 44.3393 1.27839e-09
## rno-miR-22-3p 54.7086 2.41307 0.485496 42.1150 3.79283e-09
## rno-miR-145-5p 289.3245 1.63288 0.356304 34.6466 1.44673e-07
## rno-miR-23a-3p 108.3865 1.76838 0.340275 32.4929 4.11984e-07
## rno-miR-10b-5p 91.1628 1.44507 0.292337 31.5731 6.43782e-07
## rno-miR-24-3p 58.1968 2.00698 0.440226 30.3081 1.18870e-06
## padj
## <numeric>
## rno-miR-429 6.16186e-12
## rno-miR-200b-3p 1.89753e-11
## rno-miR-10a-5p 2.47897e-11
## rno-miR-221-3p 2.95117e-11
## rno-miR-205 2.04543e-08
## rno-miR-22-3p 5.05711e-08
## rno-miR-145-5p 1.65340e-06
## rno-miR-23a-3p 4.11984e-06
## rno-miR-10b-5p 5.72250e-06
## rno-miR-24-3p 9.50960e-06Volcano plots for DESeq with likelihood ratio test
heatmap of counts
- columns clustered
- show miRNAs of top 20 mean counts
miRNA counts parsed from sRNAbench results
Repeat the above analysis on miRNA counts parsed from sRNAbench results
sample-wise heatmap
- rows and columns clustered
- label = library+dosages
PCA plots
- From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder.
- The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18) /folder.
- Compared to the 80-miRNA results from sRNAde, the plots look much different.
- The spectrum-like distribution of data over dosage PC1 also appears here.
DESeq with Wald test
Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”
- dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## Wald test p-value: dosage 50 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-200b-3p 48.78561 1.653561 0.349300 4.73393 2.20214e-06
## rno-miR-221-3p 29.41731 2.123987 0.501352 4.23652 2.27013e-05
## rno-miR-200a-3p 12.16107 2.710952 0.739204 3.66739 2.45037e-04
## rno-let-7c-5p 163.30752 1.419870 0.411958 3.44664 5.67611e-04
## rno-miR-429 19.94727 1.402210 0.415639 3.37362 7.41858e-04
## rno-miR-365-3p 7.72493 1.824171 0.568647 3.20792 1.33701e-03
## rno-miR-27a-3p 9.23401 2.119159 0.674050 3.14392 1.66702e-03
## rno-miR-205 31.13048 1.544651 0.501779 3.07835 2.08153e-03
## rno-miR-23a-3p 108.38653 0.975648 0.325839 2.99427 2.75103e-03
## rno-miR-24-3p 58.19679 1.245022 0.426453 2.91948 3.50612e-03
## padj
## <numeric>
## rno-miR-200b-3p 0.000266459
## rno-miR-221-3p 0.001373429
## rno-miR-200a-3p 0.009883165
## rno-let-7c-5p 0.017170222
## rno-miR-429 0.017952965
## rno-miR-365-3p 0.026962981
## rno-miR-27a-3p 0.028815634
## rno-miR-205 0.031483182
## rno-miR-23a-3p 0.036986119
## rno-miR-24-3p 0.042424080- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## Wald test p-value: dosage 60 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-221-3p 29.4173 3.54476 0.509464 6.95782 3.45589e-12
## rno-miR-200b-3p 48.7856 2.20791 0.359236 6.14613 7.93944e-10
## rno-miR-429 19.9473 2.46179 0.422390 5.82823 5.60192e-09
## rno-miR-10a-5p 114.3573 2.08066 0.357199 5.82492 5.71396e-09
## rno-miR-205 31.1305 2.92917 0.510933 5.73299 9.86747e-09
## rno-miR-145-5p 289.3245 1.90689 0.353461 5.39490 6.85621e-08
## rno-miR-148a-3p 7.3813 4.67085 0.868366 5.37889 7.49451e-08
## rno-miR-24-3p 58.1968 2.34345 0.436527 5.36839 7.94427e-08
## rno-miR-23a-3p 108.3865 1.72886 0.334493 5.16860 2.35849e-07
## rno-miR-22-3p 54.7086 2.40148 0.488855 4.91245 8.99431e-07
## padj
## <numeric>
## rno-miR-221-3p 6.56620e-10
## rno-miR-200b-3p 7.54247e-08
## rno-miR-429 2.71413e-07
## rno-miR-10a-5p 2.71413e-07
## rno-miR-205 3.74964e-07
## rno-miR-145-5p 1.88676e-06
## rno-miR-148a-3p 1.88676e-06
## rno-miR-24-3p 1.88676e-06
## rno-miR-23a-3p 4.97904e-06
## rno-miR-22-3p 1.70892e-05- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## Wald test p-value: dosage 75 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-200b-3p 48.7856 2.88796 0.362979 7.95627 1.77303e-15
## rno-miR-429 19.9473 3.27700 0.428205 7.65289 1.96510e-14
## rno-miR-221-3p 29.4173 3.78447 0.516494 7.32723 2.34953e-13
## rno-miR-10a-5p 114.3573 2.59699 0.359141 7.23111 4.79054e-13
## rno-miR-205 31.1305 3.20284 0.517336 6.19102 5.97753e-10
## rno-miR-148a-3p 7.3813 5.09314 0.879899 5.78833 7.10908e-09
## rno-miR-200a-3p 12.1611 4.31140 0.760779 5.66709 1.45246e-08
## rno-miR-451-5p 21.7035 4.06731 0.746619 5.44764 5.10422e-08
## rno-miR-23a-3p 108.3865 1.76816 0.338809 5.21875 1.80138e-07
## rno-miR-10b-5p 91.1628 1.44573 0.287609 5.02671 4.98955e-07
## padj
## <numeric>
## rno-miR-200b-3p 3.65244e-13
## rno-miR-429 2.02405e-12
## rno-miR-221-3p 1.61335e-11
## rno-miR-10a-5p 2.46713e-11
## rno-miR-205 2.46274e-08
## rno-miR-148a-3p 2.44078e-07
## rno-miR-200a-3p 4.27437e-07
## rno-miR-451-5p 1.31434e-06
## rno-miR-23a-3p 4.12315e-06
## rno-miR-10b-5p 1.02785e-05Volcano plots for DESeq with Wald test
DESeq with likelihood ratio test
Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.
- dosage 50mg vs 0mg results (only print the top 10 miRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-429 19.9473 1.402210 0.415639 63.2288 1.19992e-13
## rno-miR-200b-3p 48.7856 1.653561 0.349300 60.5285 4.53248e-13
## rno-miR-10a-5p 114.3573 0.918552 0.349026 59.2134 8.65507e-13
## rno-miR-221-3p 29.4173 2.123987 0.501352 56.0467 4.10555e-12
## rno-miR-205 31.1305 1.544651 0.501779 42.4798 3.17350e-09
## rno-miR-22-3p 54.7086 0.296728 0.481784 40.6700 7.68260e-09
## rno-miR-148a-3p 7.3813 2.518737 0.872444 40.5696 8.06874e-09
## rno-miR-145-5p 289.3245 0.682294 0.344846 34.8190 1.33037e-07
## rno-miR-23a-3p 108.3865 0.975648 0.325839 32.7820 3.58043e-07
## rno-miR-10b-5p 91.1628 0.301678 0.276035 32.6708 3.77894e-07
## padj
## <numeric>
## rno-miR-429 2.08787e-11
## rno-miR-200b-3p 3.94326e-11
## rno-miR-10a-5p 5.01994e-11
## rno-miR-221-3p 1.78591e-10
## rno-miR-205 1.10438e-07
## rno-miR-22-3p 2.00566e-07
## rno-miR-148a-3p 2.00566e-07
## rno-miR-145-5p 2.89355e-06
## rno-miR-23a-3p 6.57536e-06
## rno-miR-10b-5p 6.57536e-06- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-429 19.9473 2.46179 0.422390 63.2288 1.19992e-13
## rno-miR-200b-3p 48.7856 2.20791 0.359236 60.5285 4.53248e-13
## rno-miR-10a-5p 114.3573 2.08066 0.357199 59.2134 8.65507e-13
## rno-miR-221-3p 29.4173 3.54476 0.509464 56.0467 4.10555e-12
## rno-miR-205 31.1305 2.92917 0.510933 42.4798 3.17350e-09
## rno-miR-22-3p 54.7086 2.40148 0.488855 40.6700 7.68260e-09
## rno-miR-148a-3p 7.3813 4.67085 0.868366 40.5696 8.06874e-09
## rno-miR-145-5p 289.3245 1.90689 0.353461 34.8190 1.33037e-07
## rno-miR-23a-3p 108.3865 1.72886 0.334493 32.7820 3.58043e-07
## rno-miR-10b-5p 91.1628 1.05489 0.283505 32.6708 3.77894e-07
## padj
## <numeric>
## rno-miR-429 2.08787e-11
## rno-miR-200b-3p 3.94326e-11
## rno-miR-10a-5p 5.01994e-11
## rno-miR-221-3p 1.78591e-10
## rno-miR-205 1.10438e-07
## rno-miR-22-3p 2.00566e-07
## rno-miR-148a-3p 2.00566e-07
## rno-miR-145-5p 2.89355e-06
## rno-miR-23a-3p 6.57536e-06
## rno-miR-10b-5p 6.57536e-06- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange lfcSE stat pvalue
## <numeric> <numeric> <numeric> <numeric> <numeric>
## rno-miR-429 19.9473 3.27700 0.428205 63.2288 1.19992e-13
## rno-miR-200b-3p 48.7856 2.88796 0.362979 60.5285 4.53248e-13
## rno-miR-10a-5p 114.3573 2.59699 0.359141 59.2134 8.65507e-13
## rno-miR-221-3p 29.4173 3.78447 0.516494 56.0467 4.10555e-12
## rno-miR-205 31.1305 3.20284 0.517336 42.4798 3.17350e-09
## rno-miR-22-3p 54.7086 2.41256 0.493812 40.6700 7.68260e-09
## rno-miR-148a-3p 7.3813 5.09314 0.879899 40.5696 8.06874e-09
## rno-miR-145-5p 289.3245 1.63294 0.355442 34.8190 1.33037e-07
## rno-miR-23a-3p 108.3865 1.76816 0.338809 32.7820 3.58043e-07
## rno-miR-10b-5p 91.1628 1.44573 0.287609 32.6708 3.77894e-07
## padj
## <numeric>
## rno-miR-429 2.08787e-11
## rno-miR-200b-3p 3.94326e-11
## rno-miR-10a-5p 5.01994e-11
## rno-miR-221-3p 1.78591e-10
## rno-miR-205 1.10438e-07
## rno-miR-22-3p 2.00566e-07
## rno-miR-148a-3p 2.00566e-07
## rno-miR-145-5p 2.89355e-06
## rno-miR-23a-3p 6.57536e-06
## rno-miR-10b-5p 6.57536e-06Volcano plots for DESeq with likelihood ratio test
heatmap of counts
- columns clustered
- show miRNAs of top 20 mean counts
tRNA counts parsed from sRNAbench results
Repeat the above analysis on tRNA counts parsed from sRNAbench results
sample-wise heatmap
- rows and columns clustered
- label = library+dosages
PCA plots
- From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
- The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18).
- The spectrum-like distribution of data over dosage PC1 still observable.
- Library_06 as an outlier?
DESeq with Wald test
Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”
- dosage 50mg vs 0mg results (only print the top 10 tRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## Wald test p-value: dosage 50 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## Rattus_norvegicus_chr1.trna16347-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr10.trna11370-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr13.trna2187-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr13.trna3809-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr13_random.trna22-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr13_random.trna25-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr17.trna1684-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr2.trna7260-GluCTC:tRNA 6433.5762 1.142110
## Rattus_norvegicus_chr2.trna7274-GlyCCC:tRNA 377.2421 0.473923
## Rattus_norvegicus_chr16.trna1087-GluTTC:tRNA 21.3227 1.444513
## lfcSE stat
## <numeric> <numeric>
## Rattus_norvegicus_chr1.trna16347-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr10.trna11370-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr13.trna2187-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr13.trna3809-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr13_random.trna22-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr13_random.trna25-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr17.trna1684-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr2.trna7260-GluCTC:tRNA 0.331765 3.44253
## Rattus_norvegicus_chr2.trna7274-GlyCCC:tRNA 0.143668 3.29874
## Rattus_norvegicus_chr16.trna1087-GluTTC:tRNA 0.500256 2.88755
## pvalue padj
## <numeric> <numeric>
## Rattus_norvegicus_chr1.trna16347-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr10.trna11370-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr13.trna2187-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr13.trna3809-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr13_random.trna22-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr13_random.trna25-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr17.trna1684-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr2.trna7260-GluCTC:tRNA 0.000576306 0.0262940
## Rattus_norvegicus_chr2.trna7274-GlyCCC:tRNA 0.000971205 0.0393878
## Rattus_norvegicus_chr16.trna1087-GluTTC:tRNA 0.003882543 0.1417128- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## Wald test p-value: dosage 60 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 162.4158 1.78386
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 162.4158 1.78386
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 162.4158 1.78386
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 222.4611 1.27260
## Rattus_norvegicus_chrUn.trna406-LysCTT:tRNA 21.1984 1.52026
## Rattus_norvegicus_chr10.trna12028-LysCTT:tRNA 3847.5061 1.38571
## Rattus_norvegicus_chr10.trna12844-LysCTT:tRNA 3847.5061 1.38571
## Rattus_norvegicus_chr10.trna12848-LysCTT:tRNA 3847.5061 1.38571
## Rattus_norvegicus_chr10.trna12849-LysCTT:tRNA 3847.5061 1.38571
## Rattus_norvegicus_chr10.trna453-LysCTT:tRNA 3847.5061 1.38571
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 0.345438 5.16406 2.41646e-07
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 0.345438 5.16406 2.41646e-07
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 0.345438 5.16406 2.41646e-07
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 0.273486 4.65325 3.26747e-06
## Rattus_norvegicus_chrUn.trna406-LysCTT:tRNA 0.332283 4.57519 4.75787e-06
## Rattus_norvegicus_chr10.trna12028-LysCTT:tRNA 0.304203 4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna12844-LysCTT:tRNA 0.304203 4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna12848-LysCTT:tRNA 0.304203 4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna12849-LysCTT:tRNA 0.304203 4.55520 5.23355e-06
## Rattus_norvegicus_chr10.trna453-LysCTT:tRNA 0.304203 4.55520 5.23355e-06
## padj
## <numeric>
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 2.87559e-05
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 2.87559e-05
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 2.87559e-05
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 1.43721e-04
## Rattus_norvegicus_chrUn.trna406-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12028-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12844-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12848-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna12849-LysCTT:tRNA 1.43721e-04
## Rattus_norvegicus_chr10.trna453-LysCTT:tRNA 1.43721e-04- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## Wald test p-value: dosage 75 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 222.461 2.42141
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 162.416 3.02207
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 162.416 3.02207
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 162.416 3.02207
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 563.986 2.38545
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 31341.802 -1.22927
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 30684.743 -1.37082
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 28743.904 -1.47148
## Rattus_norvegicus_chr1.trna10113-ArgTCT:tRNA 8376.890 -1.30047
## Rattus_norvegicus_chr17.trna1626-SerGCT:tRNA 894.494 -1.69821
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 0.272888 8.87327 7.10318e-19
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 0.344733 8.76642 1.84442e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 0.344733 8.76642 1.84442e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 0.344733 8.76642 1.84442e-18
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 0.282356 8.44836 2.95430e-17
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 0.171136 -7.18298 6.82081e-13
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 0.197738 -6.93250 4.13463e-12
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 0.212689 -6.91846 4.56582e-12
## Rattus_norvegicus_chr1.trna10113-ArgTCT:tRNA 0.191409 -6.79418 1.08930e-11
## Rattus_norvegicus_chr17.trna1626-SerGCT:tRNA 0.250067 -6.79103 1.11337e-11
## padj
## <numeric>
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 1.68303e-16
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 1.68303e-16
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 1.68303e-16
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 1.68303e-16
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 2.15664e-15
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 4.14932e-11
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 2.08316e-10
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 2.08316e-10
## Rattus_norvegicus_chr1.trna10113-ArgTCT:tRNA 4.06380e-10
## Rattus_norvegicus_chr17.trna1626-SerGCT:tRNA 4.06380e-10Volcano plots for DESeq with Wald test
DESeq with likelihood ratio test
Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.
- dosage 50mg vs 0mg results (only print the top 10 tRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 563.986 0.202367
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 222.461 0.595371
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 162.416 0.643676
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 162.416 0.643676
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 162.416 0.643676
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 31341.802 -0.122000
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 332.893 0.179741
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 28743.904 -0.134518
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 30684.743 -0.142406
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 130.162 0.115244
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 0.276488 98.2044 3.78047e-21
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 0.268494 92.2999 7.02262e-20
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 0.340182 92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 0.340182 92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 0.340182 92.2545 7.18230e-20
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 0.166770 61.2323 3.20581e-13
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 0.286198 59.5201 7.44342e-13
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 0.207268 56.4357 3.39125e-12
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 0.192698 55.4838 5.41374e-12
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 0.183660 54.9658 6.98262e-12
## padj
## <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 1.37987e-18
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 5.24308e-18
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 1.95020e-11
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 3.88121e-11
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 1.54726e-10
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 2.19557e-10
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 2.54865e-10- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 563.986 1.045759
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 222.461 1.272599
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 162.416 1.783861
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 162.416 1.783861
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 162.416 1.783861
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 31341.802 -0.645384
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 332.893 0.937098
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 28743.904 -0.777247
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 30684.743 -0.687344
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 130.162 0.356484
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 0.282667 98.2044 3.78047e-21
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 0.273486 92.2999 7.02262e-20
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 0.345438 92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 0.345438 92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 0.345438 92.2545 7.18230e-20
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 0.171105 61.2323 3.20581e-13
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 0.292310 59.5201 7.44342e-13
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 0.212656 56.4357 3.39125e-12
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 0.197707 55.4838 5.41374e-12
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 0.186267 54.9658 6.98262e-12
## padj
## <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 1.37987e-18
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 5.24308e-18
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 1.95020e-11
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 3.88121e-11
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 1.54726e-10
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 2.19557e-10
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 2.54865e-10- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 563.986 2.38545
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 222.461 2.42141
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 162.416 3.02207
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 162.416 3.02207
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 162.416 3.02207
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 31341.802 -1.22927
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 332.893 1.94155
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 28743.904 -1.47148
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 30684.743 -1.37082
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 130.162 1.18445
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 0.282356 98.2044 3.78047e-21
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 0.272888 92.2999 7.02262e-20
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 0.344733 92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 0.344733 92.2545 7.18230e-20
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 0.344733 92.2545 7.18230e-20
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 0.171136 61.2323 3.20581e-13
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 0.292030 59.5201 7.44342e-13
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 0.212689 56.4357 3.39125e-12
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 0.197738 55.4838 5.41374e-12
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 0.185481 54.9658 6.98262e-12
## padj
## <numeric>
## Rattus_norvegicus_chr17.trna3878-ThrAGT:tRNA 1.37987e-18
## Rattus_norvegicus_chr4.trna1750-CysGCA:tRNA 5.24308e-18
## Rattus_norvegicus_chr1.trna14184-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna10836-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr10.trna2456-ThrAGT:tRNA 5.24308e-18
## Rattus_norvegicus_chr17.trna1648-SerTGA:tRNA 1.95020e-11
## Rattus_norvegicus_chr17.trna820-LysCTT:tRNA 3.88121e-11
## Rattus_norvegicus_chr5.trna491-SerAGA:tRNA 1.54726e-10
## Rattus_norvegicus_chr17.trna1642-SerAGA:tRNA 2.19557e-10
## Rattus_norvegicus_chr17.trna3843-ThrAGT:tRNA 2.54865e-10Volcano plots for DESeq with likelihood ratio test
heatmap of counts
- columns clustered
- show tRNAs of top 20 mean counts
cDNA counts parsed from sRNAbench results
Repeat the above analysis on cDNA counts parsed from sRNAbench results
sample-wise heatmap
- rows and columns clustered
- label = library+dosages
PCA plots
- From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
- The spectrum-like distribution of data over dosage PC1 still observable.
- PC2 changed after removing Library_33
DESeq with Wald test
Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”
- dosage 50mg vs 0mg results (only print the top 10 cDNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## Wald test p-value: dosage 50 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding 30.54737
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding 29.10525
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding 111.20352
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding 27.14033
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding 42.32995
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding 31.64061
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding 9.85878
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding 93.65825
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding 10.10897
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding 13.34310
## log2FoldChange
## <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding 4.11684
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding 3.59074
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding 2.85138
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding 4.05198
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding 3.72410
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding -2.90100
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding 4.68979
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding 2.89674
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding 4.89123
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding 3.31740
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding 0.811775 5.07140
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding 0.763832 4.70096
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding 0.610595 4.66984
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding 0.875880 4.62618
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding 0.808794 4.60451
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding 0.636291 -4.55923
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding 1.031961 4.54454
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding 0.646072 4.48362
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding 1.090957 4.48343
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding 0.746282 4.44523
## pvalue padj
## <numeric> <numeric>
## ENSRNOT00000081838.1-ENSRNOG00000055604.1:protein_coding 3.94892e-07 0.00067487
## ENSRNOT00000076099.1-ENSRNOG00000023577.7:protein_coding 2.58938e-06 0.00134412
## ENSRNOT00000039592.5-ENSRNOG00000022181.5:protein_coding 3.01437e-06 0.00134412
## ENSRNOT00000088851.1-ENSRNOG00000055769.1:protein_coding 3.72470e-06 0.00134412
## ENSRNOT00000036094.2-ENSRNOG00000025987.2:protein_coding 4.13430e-06 0.00134412
## ENSRNOT00000074649.2-ENSRNOG00000048205.2:protein_coding 5.13417e-06 0.00134412
## ENSRNOT00000003770.6-ENSRNOG00000002810.6:protein_coding 5.50545e-06 0.00134412
## ENSRNOT00000078734.1-ENSRNOG00000059091.1:protein_coding 7.33869e-06 0.00139476
## ENSRNOT00000078034.1-ENSRNOG00000023541.6:protein_coding 7.34515e-06 0.00139476
## ENSRNOT00000089975.1-ENSRNOG00000011180.3:protein_coding 8.77987e-06 0.00150048- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## Wald test p-value: dosage 60 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 37.3804
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 1438.2370
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 455.4459
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding 855.8283
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 145.0713
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding 144.9098
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 741.5106
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding 38.9553
## log2FoldChange
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 4.49570
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 3.71994
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 3.82316
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding 3.75779
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 3.15079
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding 3.14907
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 3.32531
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 5.48889
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 5.48889
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding 7.41695
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 0.718753 6.25486
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 0.602770 6.17140
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 0.623665 6.13016
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding 0.619567 6.06518
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 0.524450 6.00780
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding 0.528723 5.95599
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 0.569331 5.84074
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 0.941392 5.83061
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 0.941392 5.83061
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding 1.272492 5.82868
## pvalue
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 3.97868e-10
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 6.76862e-10
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 8.77935e-10
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding 1.31804e-09
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 1.88060e-09
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding 2.58505e-09
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 5.19705e-09
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 5.52260e-09
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 5.52260e-09
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding 5.58673e-09
## padj
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 8.13260e-07
## ENSRNOT00000076658.2-ENSRNOG00000051179.2:retained_intron 8.13260e-07
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 8.13260e-07
## ENSRNOT00000027493.7-ENSRNOG00000020272.7:protein_coding 9.15710e-07
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 1.04524e-06
## ENSRNOT00000057158.3-ENSRNOG00000037673.3:protein_coding 1.19731e-06
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 1.55255e-06
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 1.55255e-06
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 1.55255e-06
## ENSRNOT00000077248.1-ENSRNOG00000042411.3:protein_coding 1.55255e-06- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## Wald test p-value: dosage 75 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 102.4644
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 37.3804
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 455.4459
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 74.3853
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 922.2496
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 51.3463
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 72.4295
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 72.4939
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 741.5106
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 145.0713
## log2FoldChange
## <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.41460
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 6.08154
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 5.29364
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.38967
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 4.54005
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 5.34662
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 4.35744
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 4.35745
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 4.61055
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 4.22637
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 0.505351 8.73572
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 0.716043 8.49327
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 0.623416 8.49135
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 0.525921 8.34663
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 0.550600 8.24565
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 0.654719 8.16627
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 0.534170 8.15741
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 0.534553 8.15158
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 0.569189 8.10021
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 0.523801 8.06866
## pvalue
## <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 2.42103e-18
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.00909e-17
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 2.04250e-17
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 7.02361e-17
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 1.64269e-16
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 3.18060e-16
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 3.42292e-16
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 3.59213e-16
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 5.48627e-16
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 7.10733e-16
## padj
## <numeric>
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 8.45422e-15
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.37747e-14
## ENSRNOT00000075503.1-ENSRNOG00000049271.1:protein_coding 2.37747e-14
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 6.13161e-14
## ENSRNOT00000017075.5-ENSRNOG00000011382.6:protein_coding 1.14726e-13
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 1.56796e-13
## ENSRNOT00000088104.1-ENSRNOG00000020239.6:protein_coding 1.56796e-13
## ENSRNOT00000027430.6-ENSRNOG00000020239.6:protein_coding 1.56796e-13
## ENSRNOT00000011069.6-ENSRNOG00000008063.6:protein_coding 2.12867e-13
## ENSRNOT00000058943.4-ENSRNOG00000017127.6:protein_coding 2.48188e-13Volcano plots for DESeq with Wald test
DESeq with likelihood ratio test
Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.
- dosage 50mg vs 0mg results (only print the top 10 cDNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 37.3804
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 51.3463
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 102.4644
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 15.1979
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 23.2678
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 196.3968
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 74.3853
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 18.7590
## log2FoldChange
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.721560
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 2.224758
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 2.224758
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 1.603777
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 1.666852
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 2.014323
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 1.500488
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 0.950206
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.723242
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.081688
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 0.720490 89.6573
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 0.990685 79.6212
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 0.990685 79.6212
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 0.657661 79.1794
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 0.499279 78.8335
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.015714 77.0973
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 1.082014 74.9906
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 0.454727 73.1212
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 0.521159 72.7958
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 0.683709 72.3783
## pvalue
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.59521e-19
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.60306e-17
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 5.46045e-17
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.28680e-16
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 3.64019e-16
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 9.15627e-16
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.07504e-15
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.32092e-15
## padj
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 1.04509e-15
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.39785e-14
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.39785e-14
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 8.63660e-14
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 2.09415e-13
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 4.60904e-13
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.81022e-13
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.83575e-13- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 37.3804
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 51.3463
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 102.4644
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 15.1979
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 23.2678
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 196.3968
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 74.3853
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 18.7590
## log2FoldChange
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 4.49570
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 5.48889
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 5.48889
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 3.81202
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 2.90946
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 5.48895
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 5.55555
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 2.23837
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 2.99666
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 3.09041
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 0.718753 89.6573
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 0.941392 79.6212
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 0.941392 79.6212
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 0.656801 79.1794
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 0.506776 78.8335
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 0.958362 77.0973
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 1.019093 74.9906
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 0.463618 73.1212
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 0.527605 72.7958
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 0.664670 72.3783
## pvalue
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.59521e-19
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.60306e-17
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 5.46045e-17
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.28680e-16
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 3.64019e-16
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 9.15627e-16
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.07504e-15
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.32092e-15
## padj
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 1.04509e-15
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.39785e-14
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.39785e-14
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 8.63660e-14
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 2.09415e-13
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 4.60904e-13
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.81022e-13
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.83575e-13- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 37.3804
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 15.3069
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 51.3463
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 102.4644
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 15.1979
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 23.2678
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 196.3968
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 74.3853
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 18.7590
## log2FoldChange
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 6.08154
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 6.93784
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 6.93784
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 5.34662
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.41460
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 6.93280
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 7.31645
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 3.70414
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.38967
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.61692
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 0.716043 89.6573
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 0.937294 79.6212
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 0.937294 79.6212
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 0.654719 79.1794
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 0.505351 78.8335
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 0.954323 77.0973
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 1.015716 74.9906
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 0.462812 73.1212
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 0.525921 72.7958
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 0.659390 72.3783
## pvalue
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 2.59521e-19
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 3.70078e-17
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.60306e-17
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 5.46045e-17
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 1.28680e-16
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 3.64019e-16
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 9.15627e-16
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 1.07504e-15
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 1.32092e-15
## padj
## <numeric>
## ENSRNOT00000075682.1-ENSRNOG00000046365.1:protein_coding 1.04509e-15
## ENSRNOT00000061417.4-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000082891.1-ENSRNOG00000039969.4:protein_coding 4.39785e-14
## ENSRNOT00000064643.1-ENSRNOG00000020544.5:protein_coding 4.39785e-14
## ENSRNOT00000077651.1-ENSRNOG00000055371.1:protein_coding 4.39785e-14
## ENSRNOT00000085362.1-ENSRNOG00000057701.1:protein_coding 8.63660e-14
## ENSRNOT00000051590.2-ENSRNOG00000010235.6:protein_coding 2.09415e-13
## ENSRNOT00000011380.8-ENSRNOG00000008616.8:protein_coding 4.60904e-13
## ENSRNOT00000065043.3-ENSRNOG00000015021.7:protein_coding 4.81022e-13
## ENSRNOT00000092388.1-ENSRNOG00000052296.2:protein_coding 4.83575e-13Volcano plots for DESeq with likelihood ratio test
heatmap of counts
- columns clustered
- show cDNAs of top 20 mean counts
ncRNA counts parsed from sRNAbench results
Repeat the above analysis on ncRNA counts parsed from sRNAbench results
sample-wise heatmap
- rows and columns clustered
- label = library+dosages
PCA plots
- From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
- The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18).
- The spectrum-like distribution of data over dosage PC1 still observable.
- Library_06 as an outlier?
DESeq with Wald test
Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”
- dosage 50mg vs 0mg results (only print the top 10 ncRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## Wald test p-value: dosage 50 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 79.90376
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA 15.15926
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 141.39453
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 141.14528
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 50.65957
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 19.15829
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 6.92964
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 5.93831
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA 498.99303
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 5.73317
## log2FoldChange
## <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 2.438197
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA 3.435974
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 2.029514
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 1.933846
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 2.115309
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 1.528495
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 2.816321
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 2.961914
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA -0.767382
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 2.925478
## lfcSE
## <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 0.531396
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA 0.932182
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 0.551362
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 0.556530
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.634109
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 0.486329
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 0.950787
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 1.012509
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA 0.262394
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 1.006380
## stat
## <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 4.58829
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA 3.68595
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 3.68091
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 3.47483
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 3.33588
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 3.14293
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 2.96209
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 2.92532
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA -2.92454
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 2.90693
## pvalue
## <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 4.46893e-06
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA 2.27853e-04
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 2.32400e-04
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 5.11177e-04
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 8.50309e-04
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 1.67268e-03
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 3.05556e-03
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 3.44101e-03
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA 3.44969e-03
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 3.64994e-03
## padj
## <numeric>
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 0.000835689
## ENSRNOT00000079820.1-ENSRNOG00000056268.1:lincRNA 0.014486291
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 0.014486291
## ENSRNOT00000071067.2-ENSRNOG00000046171.3:processed_transcript 0.023897539
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.031801553
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 0.046547166
## ENSRNOT00000072266.2-ENSRNOG00000047386.3:processed_transcript 0.046547166
## ENSRNOT00000089399.1-ENSRNOG00000047386.3:processed_transcript 0.046547166
## ENSRNOT00000075536.2-ENSRNOG00000048993.2:misc_RNA 0.046547166
## ENSRNOT00000092467.1-ENSRNOG00000047386.3:processed_transcript 0.046547166- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## Wald test p-value: dosage 60 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 47.7074 1.73779
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 50.6596 3.96580
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 79.9038 3.00847
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 19.1583 2.60094
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 141.3945 3.02318
## ENSRNOT00000054649.3-ENSRNOG00000060018.1:rRNA 30.8831 1.90700
## ENSRNOT00000053226.3-ENSRNOG00000035103.3:rRNA 31.9729 1.77611
## ENSRNOT00000052795.3-ENSRNOG00000055521.1:rRNA 29.0141 1.91189
## ENSRNOT00000052439.3-ENSRNOG00000034316.3:rRNA 27.1848 1.95070
## ENSRNOT00000069467.1-ENSRNOG00000044200.1:rRNA 27.1848 1.95070
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 0.274055 6.34103
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.637457 6.22127
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 0.541196 5.55894
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 0.482084 5.39520
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 0.562714 5.37250
## ENSRNOT00000054649.3-ENSRNOG00000060018.1:rRNA 0.359619 5.30283
## ENSRNOT00000053226.3-ENSRNOG00000035103.3:rRNA 0.358567 4.95337
## ENSRNOT00000052795.3-ENSRNOG00000055521.1:rRNA 0.398831 4.79373
## ENSRNOT00000052439.3-ENSRNOG00000034316.3:rRNA 0.407980 4.78135
## ENSRNOT00000069467.1-ENSRNOG00000044200.1:rRNA 0.407980 4.78135
## pvalue padj
## <numeric> <numeric>
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 2.28241e-10 7.23525e-08
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 4.93141e-10 7.81628e-08
## ENSRNOT00000087730.1-ENSRNOG00000052433.1:lincRNA 2.71420e-08 2.86801e-06
## ENSRNOT00000074819.1-ENSRNOG00000047794.1:rRNA 6.84457e-08 4.92323e-06
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 7.76535e-08 4.92323e-06
## ENSRNOT00000054649.3-ENSRNOG00000060018.1:rRNA 1.14019e-07 6.02398e-06
## ENSRNOT00000053226.3-ENSRNOG00000035103.3:rRNA 7.29399e-07 3.30314e-05
## ENSRNOT00000052795.3-ENSRNOG00000055521.1:rRNA 1.63713e-06 4.84662e-05
## ENSRNOT00000052439.3-ENSRNOG00000034316.3:rRNA 1.74121e-06 4.84662e-05
## ENSRNOT00000069467.1-ENSRNOG00000044200.1:rRNA 1.74121e-06 4.84662e-05- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## Wald test p-value: dosage 75 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 50.6596 4.82891
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 47.7074 2.03087
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 49.8233 2.66563
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 49.8233 2.66563
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 49.8233 2.66563
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 49.8233 2.66563
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 49.8233 2.66563
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 49.8233 2.66563
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 49.8233 2.66563
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 141.3945 4.00972
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.636639 7.58500
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 0.273975 7.41263
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 0.359821 7.40820
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 0.359821 7.40820
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 0.359821 7.40820
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 0.359821 7.40820
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 0.359821 7.40820
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 0.359821 7.40820
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 0.359821 7.40820
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 0.562269 7.13132
## pvalue padj
## <numeric> <numeric>
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 3.32487e-14 5.07819e-12
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 1.23816e-13 5.07819e-12
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 1.28022e-13 5.07819e-12
## ENSRNOT00000075746.3-ENSRNOG00000047590.3:lincRNA 9.94127e-13 3.54904e-11Volcano plots for DESeq with Wald test
DESeq with likelihood ratio test
Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.
- dosage 50mg vs 0mg results (only print the top 10 ncRNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 49.8233 0.330634
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 49.8233 0.330634
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 49.8233 0.330634
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 49.8233 0.330634
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 49.8233 0.330634
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 49.8233 0.330634
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 49.8233 0.330634
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 47.7074 0.675156
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 11.7191 1.875690
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 50.6596 2.115309
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 0.365010 78.8606
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 0.365010 78.8606
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 0.365010 78.8606
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 0.365010 78.8606
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 0.365010 78.8606
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 0.365010 78.8606
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 0.365010 78.8606
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 0.278194 75.5022
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 0.940277 63.5641
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.634109 63.1738
## pvalue padj
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 2.82794e-16 1.26197e-14
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 1.01733e-13 4.03541e-12
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 1.23283e-13 4.40120e-12- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 49.8233 1.58630
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 49.8233 1.58630
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 49.8233 1.58630
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 49.8233 1.58630
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 49.8233 1.58630
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 49.8233 1.58630
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 49.8233 1.58630
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 47.7074 1.73779
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 11.7191 3.68295
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 50.6596 3.96580
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 0.361938 78.8606
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 0.361938 78.8606
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 0.361938 78.8606
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 0.361938 78.8606
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 0.361938 78.8606
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 0.361938 78.8606
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 0.361938 78.8606
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 0.274055 75.5022
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 0.911490 63.5641
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.637457 63.1738
## pvalue padj
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 2.82794e-16 1.26197e-14
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 1.01733e-13 4.03541e-12
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 1.23283e-13 4.40120e-12- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 49.8233 2.66563
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 49.8233 2.66563
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 49.8233 2.66563
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 49.8233 2.66563
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 49.8233 2.66563
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 49.8233 2.66563
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 49.8233 2.66563
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 47.7074 2.03087
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 11.7191 5.75993
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 50.6596 4.82891
## lfcSE stat
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 0.359821 78.8606
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 0.359821 78.8606
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 0.359821 78.8606
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 0.359821 78.8606
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 0.359821 78.8606
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 0.359821 78.8606
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 0.359821 78.8606
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 0.273975 75.5022
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 0.903260 63.5641
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 0.636639 63.1738
## pvalue padj
## <numeric> <numeric>
## ENSRNOT00000077643.1-ENSRNOG00000058896.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000084761.1-ENSRNOG00000056172.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000085643.1-ENSRNOG00000059852.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000087159.1-ENSRNOG00000058725.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000089050.1-ENSRNOG00000051831.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000089300.1-ENSRNOG00000059394.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000090107.1-ENSRNOG00000053888.1:rRNA 5.38795e-17 2.74785e-15
## ENSRNOT00000072497.2-ENSRNOG00000055067.1:rRNA 2.82794e-16 1.26197e-14
## ENSRNOT00000092862.1-ENSRNOG00000022163.7:antisense 1.01733e-13 4.03541e-12
## ENSRNOT00000073510.1-ENSRNOG00000046194.1:miRNA 1.23283e-13 4.40120e-12Volcano plots for DESeq with likelihood ratio test
heatmap of counts
- columns clustered
- show ncRNAs of top 20 mean counts
all RNA counts by another dataset parsed from sRNAbench results
Repeat the above analysis on a collection of different sRNA counts generated using another dataset. piRNA counts can be further extracted from the dataset.
sample-wise heatmap
- rows and columns clustered
- label = library+dosages
PCA plots
- From top to bottom: (1) groups = dosage; (2) groups = chip; (3) groups = date; (4) groups = folder
- The results seem to suggest the batch effect of chip (see chip 6) / date (see 2018-04-18).
- The spectrum-like distribution of data over dosage PC1 still observable.
- very much like the plot for cDNA, but PC2 did not change
DESeq with Wald test
Some miRNAs have NA padj values (not shown). NA padj values are generated per mechanism “If a row is filtered by automatic independent filtering, for having a low mean normalized count, then only the adjusted p value will be set to NA.”
- dosage 50mg vs 0mg results (only print the top 10 RNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## Wald test p-value: dosage 50 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## URS0000CD0A72_10116:otherRNA:Rattus_norvegicus 5116.4435 3.99323
## URS0000CCF812_10116:otherRNA:Rattus_norvegicus 5116.1125 3.99296
## URS0000CD098B_10116:otherRNA:Rattus_norvegicus 5114.4670 3.99261
## URS0000CCE881_10116:otherRNA:Rattus_norvegicus 5114.6810 3.99254
## URS0000CD0070_10116:otherRNA:Rattus_norvegicus 5114.6810 3.99254
## URS0000CD00F9_10116:otherRNA:Rattus_norvegicus 5114.7556 3.99254
## URS0000CCE385_10116:otherRNA:Rattus_norvegicus 5114.4789 3.99246
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 410.1260 3.22978
## URS00008C644C_10116:rRNA:Rattus_norvegicus 982.7875 3.37886
## URS0000B2DCD9_10116:lncRNA:Rattus_norvegicus 78.5454 3.28524
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## URS0000CD0A72_10116:otherRNA:Rattus_norvegicus 0.733740 5.44229 5.25989e-08
## URS0000CCF812_10116:otherRNA:Rattus_norvegicus 0.733700 5.44223 5.26190e-08
## URS0000CD098B_10116:otherRNA:Rattus_norvegicus 0.733716 5.44163 5.27949e-08
## URS0000CCE881_10116:otherRNA:Rattus_norvegicus 0.733708 5.44160 5.28053e-08
## URS0000CD0070_10116:otherRNA:Rattus_norvegicus 0.733708 5.44160 5.28053e-08
## URS0000CD00F9_10116:otherRNA:Rattus_norvegicus 0.733711 5.44157 5.28123e-08
## URS0000CCE385_10116:otherRNA:Rattus_norvegicus 0.733709 5.44148 5.28403e-08
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 0.599123 5.39085 7.01248e-08
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.651974 5.18251 2.18918e-07
## URS0000B2DCD9_10116:lncRNA:Rattus_norvegicus 0.649312 5.05957 4.20202e-07
## padj
## <numeric>
## URS0000CD0A72_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CCF812_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD098B_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CCE881_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD0070_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD00F9_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CCE385_10116:otherRNA:Rattus_norvegicus 0.000233697
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 0.000271374
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.000753052
## URS0000B2DCD9_10116:lncRNA:Rattus_norvegicus 0.001300904- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## Wald test p-value: dosage 60 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 982.787
## URS0000246A92_10116:rRNA:Rattus_norvegicus 2798.043
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 326.394
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 410.126
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus 168.362
## URS000096C621_10116:rRNA:Rattus_norvegicus 168.865
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5840.075
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 3193.543
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus 137.043
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus 133.566
## log2FoldChange
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 5.86837
## URS0000246A92_10116:rRNA:Rattus_norvegicus 4.58837
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 5.04313
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 4.64671
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus 5.55086
## URS000096C621_10116:rRNA:Rattus_norvegicus 5.67705
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 3.88296
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 3.93961
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus 4.96512
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus 5.62866
## lfcSE stat
## <numeric> <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.667460 8.79208
## URS0000246A92_10116:rRNA:Rattus_norvegicus 0.567077 8.09127
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 0.652237 7.73205
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 0.613641 7.57236
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus 0.742889 7.47200
## URS000096C621_10116:rRNA:Rattus_norvegicus 0.762465 7.44566
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 0.521642 7.44373
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 0.530930 7.42021
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus 0.674311 7.36325
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus 0.769077 7.31873
## pvalue
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 1.46811e-18
## URS0000246A92_10116:rRNA:Rattus_norvegicus 5.90465e-16
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 1.05832e-14
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 3.66513e-14
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus 7.89865e-14
## URS000096C621_10116:rRNA:Rattus_norvegicus 9.64616e-14
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 9.78813e-14
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 1.16938e-13
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus 1.79489e-13
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus 2.50334e-13
## padj
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 1.46107e-14
## URS0000246A92_10116:rRNA:Rattus_norvegicus 2.93815e-12
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 3.51080e-11
## URS0000CD05C5_10116:otherRNA:Rattus_norvegicus 9.11884e-11
## URS00008C5C0D_10116:rRNA:Rattus_norvegicus 1.39159e-10
## URS000096C621_10116:rRNA:Rattus_norvegicus 1.39159e-10
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 1.39159e-10
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 1.45471e-10
## URS0000CCE565_10116:otherRNA:Rattus_norvegicus 1.69252e-10
## URS0000AA6CB7_10116:lncRNA:Rattus_norvegicus 1.69252e-10- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## Wald test p-value: dosage 75 vs 0
## DataFrame with 10 rows and 6 columns
## baseMean
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 982.7875
## URS0000246A92_10116:rRNA:Rattus_norvegicus 2798.0432
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 326.3940
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5840.0751
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 97.3874
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 3193.5427
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5439.5940
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus 5527.3981
## URS00008C6232_10116:rRNA:Rattus_norvegicus 6294.9675
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 6263.2736
## log2FoldChange
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 7.43903
## URS0000246A92_10116:rRNA:Rattus_norvegicus 5.76099
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 6.43684
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 4.99015
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 6.99664
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 4.99349
## URS00008D1573_10116:rRNA:Rattus_norvegicus 4.98192
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus 5.04692
## URS00008C6232_10116:rRNA:Rattus_norvegicus 4.90935
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 4.88671
## lfcSE stat
## <numeric> <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.667377 11.14667
## URS0000246A92_10116:rRNA:Rattus_norvegicus 0.567059 10.15942
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 0.652034 9.87194
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 0.521634 9.56639
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 0.740711 9.44585
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 0.530917 9.40541
## URS00008D1573_10116:rRNA:Rattus_norvegicus 0.530315 9.39428
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus 0.538543 9.37143
## URS00008C6232_10116:rRNA:Rattus_norvegicus 0.524199 9.36543
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 0.522451 9.35343
## pvalue
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 7.43361e-29
## URS0000246A92_10116:rRNA:Rattus_norvegicus 3.00868e-24
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 5.50880e-23
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 1.10704e-21
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 3.52535e-21
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 5.18277e-21
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5.76125e-21
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus 7.15538e-21
## URS00008C6232_10116:rRNA:Rattus_norvegicus 7.57407e-21
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 8.48487e-21
## padj
## <numeric>
## URS00008C644C_10116:rRNA:Rattus_norvegicus 9.62875e-25
## URS0000246A92_10116:rRNA:Rattus_norvegicus 1.94857e-20
## URS000011E063_10116_piR-rno-3792797:piRNA:Rattus_norvegicus 2.37851e-19
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 3.58486e-18
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 9.13276e-18
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 9.63971e-18
## URS00008D1573_10116:rRNA:Rattus_norvegicus 9.63971e-18
## URS00008CB5BD_10116:rRNA:Rattus_norvegicus 9.63971e-18
## URS00008C6232_10116:rRNA:Rattus_norvegicus 9.63971e-18
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 9.63971e-18Volcano plots for DESeq with Wald test
DESeq with likelihood ratio test
Since we are running the log likelihood test, the p-values should be the same for all dosage groups. Log2FoldChange will be, however, different for each dosage group.
- dosage 50mg vs 0mg results (only print the top 10 RNAs ordered by smallest p-value first, same for below)
## log2 fold change (MLE): dosage 50 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5840.0751 1.28023
## URS00008C644C_10116:rRNA:Rattus_norvegicus 982.7875 3.37886
## URS0000246A92_10116:rRNA:Rattus_norvegicus 2798.0432 2.07124
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 3193.5427 1.27246
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5439.5940 1.24224
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 97.3874 2.10002
## URS00008C6232_10116:rRNA:Rattus_norvegicus 6294.9675 1.22645
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 6263.2736 1.22085
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 6155.9577 1.22670
## URS00008CB810_10116:rRNA:Rattus_norvegicus 6345.8351 1.21114
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 0.508620 96.6120 8.31464e-21
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.651974 95.4563 1.47319e-20
## URS0000246A92_10116:rRNA:Rattus_norvegicus 0.553095 94.4255 2.45339e-20
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 0.517829 93.8638 3.23945e-20
## URS00008D1573_10116:rRNA:Rattus_norvegicus 0.517095 93.8095 3.32772e-20
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 0.740114 93.6848 3.53948e-20
## URS00008C6232_10116:rRNA:Rattus_norvegicus 0.511101 93.5596 3.76569e-20
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 0.509397 93.4857 3.90602e-20
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 0.512656 93.3636 4.14915e-20
## URS00008CB810_10116:rRNA:Rattus_norvegicus 0.511252 93.2325 4.42720e-20
## padj
## <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008C644C_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS0000246A92_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6232_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CB810_10116:rRNA:Rattus_norvegicus 5.5086e-17- dosage 60mg vs 0mg results
## log2 fold change (MLE): dosage 60 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5840.0751 3.88296
## URS00008C644C_10116:rRNA:Rattus_norvegicus 982.7875 5.86837
## URS0000246A92_10116:rRNA:Rattus_norvegicus 2798.0432 4.58837
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 3193.5427 3.93961
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5439.5940 3.86076
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 97.3874 5.38486
## URS00008C6232_10116:rRNA:Rattus_norvegicus 6294.9675 3.79468
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 6263.2736 3.78503
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 6155.9577 3.83198
## URS00008CB810_10116:rRNA:Rattus_norvegicus 6345.8351 3.80183
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 0.521642 96.6120 8.31464e-21
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.667460 95.4563 1.47319e-20
## URS0000246A92_10116:rRNA:Rattus_norvegicus 0.567077 94.4255 2.45339e-20
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 0.530930 93.8638 3.23945e-20
## URS00008D1573_10116:rRNA:Rattus_norvegicus 0.530324 93.8095 3.32772e-20
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 0.741492 93.6848 3.53948e-20
## URS00008C6232_10116:rRNA:Rattus_norvegicus 0.524207 93.5596 3.76569e-20
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 0.522459 93.4857 3.90602e-20
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 0.525797 93.3636 4.14915e-20
## URS00008CB810_10116:rRNA:Rattus_norvegicus 0.524363 93.2325 4.42720e-20
## padj
## <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008C644C_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS0000246A92_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6232_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CB810_10116:rRNA:Rattus_norvegicus 5.5086e-17- dosage 75mg vs 0mg results
## log2 fold change (MLE): dosage 75 vs 0
## LRT p-value: '~ dosage' vs '~ 1'
## DataFrame with 10 rows and 6 columns
## baseMean log2FoldChange
## <numeric> <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5840.0751 4.99015
## URS00008C644C_10116:rRNA:Rattus_norvegicus 982.7875 7.43903
## URS0000246A92_10116:rRNA:Rattus_norvegicus 2798.0432 5.76099
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 3193.5427 4.99349
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5439.5940 4.98192
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 97.3874 6.99664
## URS00008C6232_10116:rRNA:Rattus_norvegicus 6294.9675 4.90935
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 6263.2736 4.88671
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 6155.9577 4.91559
## URS00008CB810_10116:rRNA:Rattus_norvegicus 6345.8351 4.89185
## lfcSE stat pvalue
## <numeric> <numeric> <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 0.521634 96.6120 8.31464e-21
## URS00008C644C_10116:rRNA:Rattus_norvegicus 0.667377 95.4563 1.47319e-20
## URS0000246A92_10116:rRNA:Rattus_norvegicus 0.567059 94.4255 2.45339e-20
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 0.530917 93.8638 3.23945e-20
## URS00008D1573_10116:rRNA:Rattus_norvegicus 0.530315 93.8095 3.32772e-20
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 0.740711 93.6848 3.53948e-20
## URS00008C6232_10116:rRNA:Rattus_norvegicus 0.524199 93.5596 3.76569e-20
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 0.522451 93.4857 3.90602e-20
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 0.525789 93.3636 4.14915e-20
## URS00008CB810_10116:rRNA:Rattus_norvegicus 0.524355 93.2325 4.42720e-20
## padj
## <numeric>
## URS00008CFDE4_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008C644C_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS0000246A92_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6A58_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008D1573_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS0000CCEC4C_10116:otherRNA:Rattus_norvegicus 5.5086e-17
## URS00008C6232_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CA49B_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CC58A_10116:rRNA:Rattus_norvegicus 5.5086e-17
## URS00008CB810_10116:rRNA:Rattus_norvegicus 5.5086e-17Volcano plots for DESeq with likelihood ratio test
heatmap of counts
- columns clustered
- show RNAs of top 20 mean counts
